8TO2

Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)

PDB DOI: https://doi.org/10.2210/pdb8TO2/pdb
EM Map EMD-41434: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Synechocystis sp. PCC 6803
Mutation(s): No

Deposited: 2023-08-02 Released: 2024-04-17
Deposition Author(s): Sauer, P.V., Sutter, M., Cupellini, L.
Funding Organization(s): European Research Council (ERC), Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Czech Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes.

Sauer, P.V., Cupellini, L., Sutter, M., Bondanza, M., Dominguez Martin, M.A., Kirst, H., Bina, D., Koh, A.F., Kotecha, A., Greber, B.J., Nogales, E., Polivka, T., Mennucci, B., Kerfeld, C.A.

(2024) Sci Adv 10: eadk7535-eadk7535

PubMed: 38578996 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adk7535
Primary Citation of Related Structures:
8TO2, 8TO5, 8TPJ, 8TRO

PubMed Abstract:
Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.

Organizational Affiliation

California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.

Macromolecule Content

Total Structure Weight: 607.99 kDa
Atom Count: 37,185
Modelled Residue Count: 4,737
Deposited Residue Count: 5,428
Unique protein chains: 9

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycobiliprotein ApcE	A	896	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for Q55544 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55544 Go to UniProtKB: Q55544
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q55544
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Orange carotenoid-binding protein	B	317	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for P74102 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P74102 Go to UniProtKB: P74102
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P74102
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core	C, Q [auth c]	67	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for Q02925 (Synechocystis sp. (strain PCC 6714)) Explore Q02925 Go to UniProtKB: Q02925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02925
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin alpha chain	D F H J L D, F, H, J, L, N, T [auth f], V [auth h], X [auth j], Z [auth l]	161	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for Q01951 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q01951 Go to UniProtKB: Q01951
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01951
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin beta chain	AA [auth m] E G I K AA [auth m], E, G, I, K, M, O, S [auth e], U [auth g], W [auth i], Y [auth k]	161	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for Q01952 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q01952 Go to UniProtKB: Q01952
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01952
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycobilisome rod-core linker polypeptide CpcG	P	249	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for P73093 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P73093 Go to UniProtKB: P73093
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P73093
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin subunit alpha-B	R [auth d]	161	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for P72870 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72870 Go to UniProtKB: P72870
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72870
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin subunit beta-18	BA [auth o]	169	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for P74551 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P74551 Go to UniProtKB: P74551
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P74551
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-2	CA [auth p]	121	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for A0A6P1VGS4 (Synechocystis sp. CACIAM 05) Explore A0A6P1VGS4 Go to UniProtKB: A0A6P1VGS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P1VGS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download Ideal Coordinates CCD File SDF format, chain AB [auth m] SDF format, chain BB [auth o] SDF format, chain DA [auth A] SDF format, chain FA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth J] SDF format, chain MA [auth K] SDF format, chain NA [auth L] SDF format, chain OA [auth M] SDF format, chain PA [auth N] SDF format, chain QA [auth O] SDF format, chain RA [auth d] SDF format, chain SA [auth e] SDF format, chain TA [auth f] SDF format, chain UA [auth g] SDF format, chain VA [auth h] SDF format, chain WA [auth i] SDF format, chain XA [auth j] SDF format, chain YA [auth k] SDF format, chain ZA [auth l] MOL2 format, chain AB [auth m] MOL2 format, chain BB [auth o] MOL2 format, chain DA [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain NA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain PA [auth N] MOL2 format, chain QA [auth O] MOL2 format, chain RA [auth d] MOL2 format, chain SA [auth e] MOL2 format, chain TA [auth f] MOL2 format, chain UA [auth g] MOL2 format, chain VA [auth h] MOL2 format, chain WA [auth i] MOL2 format, chain XA [auth j] MOL2 format, chain YA [auth k] MOL2 format, chain ZA [auth l]	AB [auth m] BB [auth o] DA [auth A] FA [auth D] GA [auth E] AB [auth m], BB [auth o], DA [auth A], FA [auth D], GA [auth E], HA [auth F], IA [auth G], JA [auth H], KA [auth I], LA [auth J], MA [auth K], NA [auth L], OA [auth M], PA [auth N], QA [auth O], RA [auth d], SA [auth e], TA [auth f], UA [auth g], VA [auth h], WA [auth i], XA [auth j], YA [auth k], ZA [auth l]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AB [auth m] Focus chain BB [auth o] Focus chain DA [auth A] Focus chain FA [auth D] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain QA [auth O] Focus chain RA [auth d] Focus chain SA [auth e] Focus chain TA [auth f] Focus chain UA [auth g] Focus chain VA [auth h] Focus chain WA [auth i] Focus chain XA [auth j] Focus chain YA [auth k] Focus chain ZA [auth l] Interactions & Density Focus chain AB [auth m] Focus chain BB [auth o] Focus chain DA [auth A] Focus chain FA [auth D] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain QA [auth O] Focus chain RA [auth d] Focus chain SA [auth e] Focus chain TA [auth f] Focus chain UA [auth g] Focus chain VA [auth h] Focus chain WA [auth i] Focus chain XA [auth j] Focus chain YA [auth k] Focus chain ZA [auth l]
45D (Subject of Investigation/LOI) Query on 45D Download Ideal Coordinates CCD File SDF format, chain EA [auth B] MOL2 format, chain EA [auth B]	EA [auth B]	beta,beta-carotene-4,4'-dione C₄₀ H₅₂ O₂ FDSDTBUPSURDBL-DKLMTRRASA-N		Interactions Focus chain EA [auth B] Interactions & Density Focus chain EA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Sauer, P.V.

Sutter, M.

Cupellini, L.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	Grant ERC-AdG 786714 (LIFETimeS)
Department of Energy (DOE, United States)	United States	DE-SC0020606
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM127018
Czech Science Foundation	Czech Republic	19-28323X

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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8TO2

Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)

Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes.

Entity ID: 1

UniProt

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Sequence Annotations

Entity ID: 2

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)